Hi Manoj,

No. APPLY CHANGES does not delete the data from bonze if key/data is not present in source. It will delete it based on the value of some incoming field. Something like a status (="Delete") or such. 

If no status can be provided from source then you will need to execute the deletes once again in each layer. Make sure that you set the skipChangeCommits flag to true so the streams ignore any deletes and updates. Streaming is append only and hence does not expect any deletes or updates in source.  Link

A common example is if you are clearing out old data from the source tables, You will need to do this for all layers. DLT will not do it automatically for you.